Hi All I'm receiving an error with mri_cvs_register from FS 5.1 on a 64-bit Mac 10.6.7 system and was hoping for some help. It's the same error with the 3 subjects I've tried it on, and occurs both before and after using the mri_cvs_register that was updated on Jun 10th. I'm including the last few lines of the log file. Thanks David
---------LOG----------
step = 12 =============== elt_vol= 15.0625 Constructing Delaunay tetrahedralization. Delaunay seconds: 7.9e-05 Creating surface mesh. Perturbing vertices. Delaunizing segments. Constraining facets. Segment and facet seconds: 0.000686 Removing unwanted tetrahedra. Hole seconds: 3.3e-05 Repairing mesh. Repair seconds: 6.9e-05 Adding Steiner points to enforce quality. Quality seconds: 4.27942 Smoothing mesh. Smooth seconds: 0.299788
Writing nodes. Writing elements. Writing faces.
Output seconds: 0.036639 Total running seconds: 4.61682
Statistics:
Input points: 8 Input facets: 6 Input holes: 0 Input regions: 0
Mesh points: 81870 Mesh tetrahedra: 491585 Mesh faces: 995562 Mesh subfaces: 24784 Mesh subsegments: 530
Saving nodes to iteration.node Saving elements to iteration.ele Saving faces to iteration.face mesh nodes = 81870 mesh elts = 491585 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 count inserted = 100000 elapsed = 0.302 seconds element count = 1128168 count inserted = 200000 elapsed = 0.496 seconds element count = 3256402 count inserted = 300000 elapsed = 0.411 seconds element count = 5222879 count inserted = 400000 elapsed = 0.343 seconds element count = 7039018 done building octree - total elements = 8705605 penalty_weight = 1000 setting bc 205.891 174.948 225.515 -> 0 0 0 instead 205.881 174.938 225.505 -> norm = 0.0173205 setting bc 205.891 174.948 27.6148 -> 0 0 0 instead 205.881 174.938 27.6248 -> norm = 0.0173205 setting bc 205.891 35.1985 225.515 -> 0 0 0 instead 205.881 35.2085 225.505 -> norm = 0.0173205 setting bc 205.891 35.1985 27.6148 -> 0 0 0 instead 205.881 35.2085 27.6248 -> norm = 0.0173205 setting bc 52.3002 174.948 225.515 -> 0 0 0 instead 52.3102 174.938 225.505 -> norm = 0.0173205 setting bc 52.3002 174.948 27.6148 -> 0 0 0 instead 52.3102 174.938 27.6248 -> norm = 0.0173205 setting bc 52.3002 35.1985 225.515 -> 0 0 0 instead 52.3102 35.2085 225.505 -> norm = 0.0173205 setting bc 52.3002 35.1985 27.6148 -> 0 0 0 instead 52.3102 35.2085 27.6248 -> norm = 0.0173205 computing statistics for the displacement application error average norm of error in placement = 0.0173205 iterating done with candidates Active BCs = 92200 Total BCs = 548640 no-eqs = 245610 surf2vol(4634) malloc: *** mmap(size=295714816) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Out of memory. This could be due to allocating [0]PETSC ERROR: too large an object or bleeding by not properly [0]PETSC ERROR: destroying unneeded objects. [0]PETSC ERROR: Memory allocated 0 Memory used by process 0 [0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info. [0]PETSC ERROR: Memory requested 295714444! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: surf2vol on a darwin9.8 named Psytechs-Mac-Pro.local by dbrang Fri Jun 17 17:23:37 2011 [0]PETSC ERROR: Libraries linked from /usr/pubsw/packages/petsc/current/src/petsc-2.3.3-p13/lib/darwin9.8.0-c-opt [0]PETSC ERROR: Configure run at Thu Feb 17 18:27:43 2011 [0]PETSC ERROR: Configure options --with-mpi-dir=/usr/pubsw/packages/petsc/current/src/mpilatestbuild/ --with-shared=0 --with-debugging=0 --with-fc=gfortran --with-cc=gcc [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: PetscMallocAlign() line 61 in src/sys/memory/mal.c [0]PETSC ERROR: MatSeqAIJSetPreallocation_SeqAIJ() line 2818 in src/mat/impls/aij/seq/aij.c [0]PETSC ERROR: MatCreateSeqAIJ() line 2703 in src/mat/impls/aij/seq/aij.c [0]PETSC ERROR: TSolver::setup_matrix() line 658 in unknowndirectory/solver.h [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 10 BUS: Bus Error, possibly illegal memory access [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Sig...: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Signal received! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: surf2vol on a darwin9.8 named Psytechs-Mac-Pro.local by dbrang Fri Jun 17 17:23:37 2011 [0]PETSC ERROR: Libraries linked from /usr/pubsw/packages/petsc/current/src/petsc-2.3.3-p13/lib/darwin9.8.0-c-opt [0]PETSC ERROR: Configure run at Thu Feb 17 18:27:43 2011 [0]PETSC ERROR: Configure options --with-mpi-dir=/usr/pubsw/packages/petsc/current/src/mpilatestbuild/ --with-shared=0 --with-debugging=0 --with-fc=gfortran --with-cc=gcc [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
Hi David,
I usually get PETSC errors when I have files from a previous unsuccessful runs of cvs and mri_cvs_register is trying to overwrite the same set of files. I've always found that deleting all the cvs related files before starting mri_cvs_register from scratch usually solves the issue. You can try doing that to see if it works for you.
Thanks, Priti
Hi All I'm receiving an error with mri_cvs_register from FS 5.1 on a 64-bit Mac 10.6.7 system and was hoping for some help. It's the same error with the 3 subjects I've tried it on, and occurs both before and after using the mri_cvs_register that was updated on Jun 10th. I'm including the last few lines of the log file. Thanks David
---------LOG----------
step = 12
elt_vol= 15.0625 Constructing Delaunay tetrahedralization. Delaunay seconds: 7.9e-05 Creating surface mesh. Perturbing vertices. Delaunizing segments. Constraining facets. Segment and facet seconds: 0.000686 Removing unwanted tetrahedra. Hole seconds: 3.3e-05 Repairing mesh. Repair seconds: 6.9e-05 Adding Steiner points to enforce quality. Quality seconds: 4.27942 Smoothing mesh. Smooth seconds: 0.299788
Writing nodes. Writing elements. Writing faces.
Output seconds: 0.036639 Total running seconds: 4.61682
Statistics:
Input points: 8 Input facets: 6 Input holes: 0 Input regions: 0
Mesh points: 81870 Mesh tetrahedra: 491585 Mesh faces: 995562 Mesh subfaces: 24784 Mesh subsegments: 530
Saving nodes to iteration.node Saving elements to iteration.ele Saving faces to iteration.face mesh nodes = 81870 mesh elts = 491585 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 count inserted = 100000 elapsed = 0.302 seconds element count = 1128168 count inserted = 200000 elapsed = 0.496 seconds element count = 3256402 count inserted = 300000 elapsed = 0.411 seconds element count = 5222879 count inserted = 400000 elapsed = 0.343 seconds element count = 7039018 done building octree - total elements = 8705605 penalty_weight = 1000 setting bc 205.891 174.948 225.515 -> 0 0 0 instead 205.881 174.938 225.505 -> norm = 0.0173205 setting bc 205.891 174.948 27.6148 -> 0 0 0 instead 205.881 174.938 27.6248 -> norm = 0.0173205 setting bc 205.891 35.1985 225.515 -> 0 0 0 instead 205.881 35.2085 225.505 -> norm = 0.0173205 setting bc 205.891 35.1985 27.6148 -> 0 0 0 instead 205.881 35.2085 27.6248 -> norm = 0.0173205 setting bc 52.3002 174.948 225.515 -> 0 0 0 instead 52.3102 174.938 225.505 -> norm = 0.0173205 setting bc 52.3002 174.948 27.6148 -> 0 0 0 instead 52.3102 174.938 27.6248 -> norm = 0.0173205 setting bc 52.3002 35.1985 225.515 -> 0 0 0 instead 52.3102 35.2085 225.505 -> norm = 0.0173205 setting bc 52.3002 35.1985 27.6148 -> 0 0 0 instead 52.3102 35.2085 27.6248 -> norm = 0.0173205 computing statistics for the displacement application error average norm of error in placement = 0.0173205 iterating done with candidates Active BCs = 92200 Total BCs = 548640 no-eqs = 245610 surf2vol(4634) malloc: *** mmap(size=295714816) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug [0]PETSC ERROR: --------------------- Error Message
[0]PETSC ERROR: Out of memory. This could be due to allocating [0]PETSC ERROR: too large an object or bleeding by not properly [0]PETSC ERROR: destroying unneeded objects. [0]PETSC ERROR: Memory allocated 0 Memory used by process 0 [0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info. [0]PETSC ERROR: Memory requested 295714444! [0]PETSC ERROR:
[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR:
[0]PETSC ERROR: surf2vol on a darwin9.8 named Psytechs-Mac-Pro.local by dbrang Fri Jun 17 17:23:37 2011 [0]PETSC ERROR: Libraries linked from /usr/pubsw/packages/petsc/current/src/petsc-2.3.3-p13/lib/darwin9.8.0-c-opt [0]PETSC ERROR: Configure run at Thu Feb 17 18:27:43 2011 [0]PETSC ERROR: Configure options --with-mpi-dir=/usr/pubsw/packages/petsc/current/src/mpilatestbuild/ --with-shared=0 --with-debugging=0 --with-fc=gfortran --with-cc=gcc [0]PETSC ERROR:
[0]PETSC ERROR: PetscMallocAlign() line 61 in src/sys/memory/mal.c [0]PETSC ERROR: MatSeqAIJSetPreallocation_SeqAIJ() line 2818 in src/mat/impls/aij/seq/aij.c [0]PETSC ERROR: MatCreateSeqAIJ() line 2703 in src/mat/impls/aij/seq/aij.c [0]PETSC ERROR: TSolver::setup_matrix() line 658 in unknowndirectory/solver.h [0]PETSC ERROR:
[0]PETSC ERROR: Caught signal number 10 BUS: Bus Error, possibly illegal memory access [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Sig...: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: --------------------- Error Message
[0]PETSC ERROR: Signal received! [0]PETSC ERROR:
[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR:
[0]PETSC ERROR: surf2vol on a darwin9.8 named Psytechs-Mac-Pro.local by dbrang Fri Jun 17 17:23:37 2011 [0]PETSC ERROR: Libraries linked from /usr/pubsw/packages/petsc/current/src/petsc-2.3.3-p13/lib/darwin9.8.0-c-opt [0]PETSC ERROR: Configure run at Thu Feb 17 18:27:43 2011 [0]PETSC ERROR: Configure options --with-mpi-dir=/usr/pubsw/packages/petsc/current/src/mpilatestbuild/ --with-shared=0 --with-debugging=0 --with-fc=gfortran --with-cc=gcc [0]PETSC ERROR:
[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks for the advice Priti, I deleted the old cvs files and re-ran but still no luck. I also tried a new subject on a different Mac (still 10.6.7) and received the same error. Thanks David
On Mon, Jun 20, 2011 at 12:56 PM, rspriti@nmr.mgh.harvard.edu wrote:
Hi David,
I usually get PETSC errors when I have files from a previous unsuccessful runs of cvs and mri_cvs_register is trying to overwrite the same set of files. I've always found that deleting all the cvs related files before starting mri_cvs_register from scratch usually solves the issue. You can try doing that to see if it works for you.
Thanks, Priti
Hi All I'm receiving an error with mri_cvs_register from FS 5.1 on a 64-bit Mac 10.6.7 system and was hoping for some help. It's the same error with the
3
subjects I've tried it on, and occurs both before and after using the mri_cvs_register that was updated on Jun 10th. I'm including the last few lines of the log file. Thanks David
---------LOG----------
step = 12
elt_vol= 15.0625 Constructing Delaunay tetrahedralization. Delaunay seconds: 7.9e-05 Creating surface mesh. Perturbing vertices. Delaunizing segments. Constraining facets. Segment and facet seconds: 0.000686 Removing unwanted tetrahedra. Hole seconds: 3.3e-05 Repairing mesh. Repair seconds: 6.9e-05 Adding Steiner points to enforce quality. Quality seconds: 4.27942 Smoothing mesh. Smooth seconds: 0.299788
Writing nodes. Writing elements. Writing faces.
Output seconds: 0.036639 Total running seconds: 4.61682
Statistics:
Input points: 8 Input facets: 6 Input holes: 0 Input regions: 0
Mesh points: 81870 Mesh tetrahedra: 491585 Mesh faces: 995562 Mesh subfaces: 24784 Mesh subsegments: 530
Saving nodes to iteration.node Saving elements to iteration.ele Saving faces to iteration.face mesh nodes = 81870 mesh elts = 491585 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 count inserted = 100000 elapsed = 0.302 seconds element count = 1128168 count inserted = 200000 elapsed = 0.496 seconds element count = 3256402 count inserted = 300000 elapsed = 0.411 seconds element count = 5222879 count inserted = 400000 elapsed = 0.343 seconds element count = 7039018 done building octree - total elements = 8705605 penalty_weight = 1000 setting bc 205.891 174.948 225.515 -> 0 0 0 instead 205.881 174.938 225.505 -> norm = 0.0173205 setting bc 205.891 174.948 27.6148 -> 0 0 0 instead 205.881 174.938 27.6248 -> norm = 0.0173205 setting bc 205.891 35.1985 225.515 -> 0 0 0 instead 205.881 35.2085 225.505 -> norm = 0.0173205 setting bc 205.891 35.1985 27.6148 -> 0 0 0 instead 205.881 35.2085 27.6248 -> norm = 0.0173205 setting bc 52.3002 174.948 225.515 -> 0 0 0 instead 52.3102 174.938 225.505 -> norm = 0.0173205 setting bc 52.3002 174.948 27.6148 -> 0 0 0 instead 52.3102 174.938 27.6248 -> norm = 0.0173205 setting bc 52.3002 35.1985 225.515 -> 0 0 0 instead 52.3102 35.2085 225.505 -> norm = 0.0173205 setting bc 52.3002 35.1985 27.6148 -> 0 0 0 instead 52.3102 35.2085 27.6248 -> norm = 0.0173205 computing statistics for the displacement application error average norm of error in placement = 0.0173205 iterating done with candidates Active BCs = 92200 Total BCs = 548640 no-eqs = 245610 surf2vol(4634) malloc: *** mmap(size=295714816) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug [0]PETSC ERROR: --------------------- Error Message
[0]PETSC ERROR: Out of memory. This could be due to allocating [0]PETSC ERROR: too large an object or bleeding by not properly [0]PETSC ERROR: destroying unneeded objects. [0]PETSC ERROR: Memory allocated 0 Memory used by process 0 [0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info. [0]PETSC ERROR: Memory requested 295714444! [0]PETSC ERROR:
[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15
17:29:26
CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR:
[0]PETSC ERROR: surf2vol on a darwin9.8 named Psytechs-Mac-Pro.local by dbrang Fri Jun 17 17:23:37 2011 [0]PETSC ERROR: Libraries linked from
/usr/pubsw/packages/petsc/current/src/petsc-2.3.3-p13/lib/darwin9.8.0-c-opt
[0]PETSC ERROR: Configure run at Thu Feb 17 18:27:43 2011 [0]PETSC ERROR: Configure options --with-mpi-dir=/usr/pubsw/packages/petsc/current/src/mpilatestbuild/ --with-shared=0 --with-debugging=0 --with-fc=gfortran --with-cc=gcc [0]PETSC ERROR:
[0]PETSC ERROR: PetscMallocAlign() line 61 in src/sys/memory/mal.c [0]PETSC ERROR: MatSeqAIJSetPreallocation_SeqAIJ() line 2818 in src/mat/impls/aij/seq/aij.c [0]PETSC ERROR: MatCreateSeqAIJ() line 2703 in
src/mat/impls/aij/seq/aij.c
[0]PETSC ERROR: TSolver::setup_matrix() line 658 in unknowndirectory/solver.h [0]PETSC ERROR:
[0]PETSC ERROR: Caught signal number 10 BUS: Bus Error, possibly illegal memory access [0]PETSC ERROR: Try option -start_in_debugger or
-on_error_attach_debugger
[0]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Sig... :
or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
and
run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: --------------------- Error Message
[0]PETSC ERROR: Signal received! [0]PETSC ERROR:
[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15
17:29:26
CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR:
[0]PETSC ERROR: surf2vol on a darwin9.8 named Psytechs-Mac-Pro.local by dbrang Fri Jun 17 17:23:37 2011 [0]PETSC ERROR: Libraries linked from
/usr/pubsw/packages/petsc/current/src/petsc-2.3.3-p13/lib/darwin9.8.0-c-opt
[0]PETSC ERROR: Configure run at Thu Feb 17 18:27:43 2011 [0]PETSC ERROR: Configure options --with-mpi-dir=/usr/pubsw/packages/petsc/current/src/mpilatestbuild/ --with-shared=0 --with-debugging=0 --with-fc=gfortran --with-cc=gcc [0]PETSC ERROR:
[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi David,
FreeSurfer's binaries for MAC are still 32-bit and apparently cvs tries to allocate more that is possible. The lines of the error code below suggest that. I had the same problem and had to opt for x86_64 linux binaries, where the cvs runs fine. It needs ~ 6 GB of memory and takes ~ 2 days to finish.
Regards,
Martin
surf2vol(4634) malloc: *** mmap(size=295714816) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Out of memory. This could be due to allocating [0]PETSC ERROR: too large an object or bleeding by not properly
On Mon, Jun 20, 2011 at 11:34 PM, David Brang dbrang@gmail.com wrote:
Thanks for the advice Priti, I deleted the old cvs files and re-ran but still no luck. I also tried a new subject on a different Mac (still 10.6.7) and received the same error. Thanks David
On Mon, Jun 20, 2011 at 12:56 PM, rspriti@nmr.mgh.harvard.edu wrote:
Hi David,
I usually get PETSC errors when I have files from a previous unsuccessful runs of cvs and mri_cvs_register is trying to overwrite the same set of files. I've always found that deleting all the cvs related files before starting mri_cvs_register from scratch usually solves the issue. You can try doing that to see if it works for you.
Thanks, Priti
Hi All I'm receiving an error with mri_cvs_register from FS 5.1 on a 64-bit Mac 10.6.7 system and was hoping for some help. It's the same error with the 3 subjects I've tried it on, and occurs both before and after using the mri_cvs_register that was updated on Jun 10th. I'm including the last few lines of the log file. Thanks David
---------LOG----------
step = 12
elt_vol= 15.0625 Constructing Delaunay tetrahedralization. Delaunay seconds: 7.9e-05 Creating surface mesh. Perturbing vertices. Delaunizing segments. Constraining facets. Segment and facet seconds: 0.000686 Removing unwanted tetrahedra. Hole seconds: 3.3e-05 Repairing mesh. Repair seconds: 6.9e-05 Adding Steiner points to enforce quality. Quality seconds: 4.27942 Smoothing mesh. Smooth seconds: 0.299788
Writing nodes. Writing elements. Writing faces.
Output seconds: 0.036639 Total running seconds: 4.61682
Statistics:
Input points: 8 Input facets: 6 Input holes: 0 Input regions: 0
Mesh points: 81870 Mesh tetrahedra: 491585 Mesh faces: 995562 Mesh subfaces: 24784 Mesh subsegments: 530
Saving nodes to iteration.node Saving elements to iteration.ele Saving faces to iteration.face mesh nodes = 81870 mesh elts = 491585 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 count inserted = 100000 elapsed = 0.302 seconds element count = 1128168 count inserted = 200000 elapsed = 0.496 seconds element count = 3256402 count inserted = 300000 elapsed = 0.411 seconds element count = 5222879 count inserted = 400000 elapsed = 0.343 seconds element count = 7039018 done building octree - total elements = 8705605 penalty_weight = 1000 setting bc 205.891 174.948 225.515 -> 0 0 0 instead 205.881 174.938 225.505 -> norm = 0.0173205 setting bc 205.891 174.948 27.6148 -> 0 0 0 instead 205.881 174.938 27.6248 -> norm = 0.0173205 setting bc 205.891 35.1985 225.515 -> 0 0 0 instead 205.881 35.2085 225.505 -> norm = 0.0173205 setting bc 205.891 35.1985 27.6148 -> 0 0 0 instead 205.881 35.2085 27.6248 -> norm = 0.0173205 setting bc 52.3002 174.948 225.515 -> 0 0 0 instead 52.3102 174.938 225.505 -> norm = 0.0173205 setting bc 52.3002 174.948 27.6148 -> 0 0 0 instead 52.3102 174.938 27.6248 -> norm = 0.0173205 setting bc 52.3002 35.1985 225.515 -> 0 0 0 instead 52.3102 35.2085 225.505 -> norm = 0.0173205 setting bc 52.3002 35.1985 27.6148 -> 0 0 0 instead 52.3102 35.2085 27.6248 -> norm = 0.0173205 computing statistics for the displacement application error average norm of error in placement = 0.0173205 iterating done with candidates Active BCs = 92200 Total BCs = 548640 no-eqs = 245610 surf2vol(4634) malloc: *** mmap(size=295714816) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug [0]PETSC ERROR: --------------------- Error Message
[0]PETSC ERROR: Out of memory. This could be due to allocating [0]PETSC ERROR: too large an object or bleeding by not properly [0]PETSC ERROR: destroying unneeded objects. [0]PETSC ERROR: Memory allocated 0 Memory used by process 0 [0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info. [0]PETSC ERROR: Memory requested 295714444! [0]PETSC ERROR:
[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR:
[0]PETSC ERROR: surf2vol on a darwin9.8 named Psytechs-Mac-Pro.local by dbrang Fri Jun 17 17:23:37 2011 [0]PETSC ERROR: Libraries linked from
/usr/pubsw/packages/petsc/current/src/petsc-2.3.3-p13/lib/darwin9.8.0-c-opt [0]PETSC ERROR: Configure run at Thu Feb 17 18:27:43 2011 [0]PETSC ERROR: Configure options --with-mpi-dir=/usr/pubsw/packages/petsc/current/src/mpilatestbuild/ --with-shared=0 --with-debugging=0 --with-fc=gfortran --with-cc=gcc [0]PETSC ERROR:
[0]PETSC ERROR: PetscMallocAlign() line 61 in src/sys/memory/mal.c [0]PETSC ERROR: MatSeqAIJSetPreallocation_SeqAIJ() line 2818 in src/mat/impls/aij/seq/aij.c [0]PETSC ERROR: MatCreateSeqAIJ() line 2703 in src/mat/impls/aij/seq/aij.c [0]PETSC ERROR: TSolver::setup_matrix() line 658 in unknowndirectory/solver.h [0]PETSC ERROR:
[0]PETSC ERROR: Caught signal number 10 BUS: Bus Error, possibly illegal memory access [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Sig...: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: --------------------- Error Message
[0]PETSC ERROR: Signal received! [0]PETSC ERROR:
[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR:
[0]PETSC ERROR: surf2vol on a darwin9.8 named Psytechs-Mac-Pro.local by dbrang Fri Jun 17 17:23:37 2011 [0]PETSC ERROR: Libraries linked from
/usr/pubsw/packages/petsc/current/src/petsc-2.3.3-p13/lib/darwin9.8.0-c-opt [0]PETSC ERROR: Configure run at Thu Feb 17 18:27:43 2011 [0]PETSC ERROR: Configure options --with-mpi-dir=/usr/pubsw/packages/petsc/current/src/mpilatestbuild/ --with-shared=0 --with-debugging=0 --with-fc=gfortran --with-cc=gcc [0]PETSC ERROR:
[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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